Posts Tagged ‘Voting’

Molecules of the year? Pnictogen chains and 16 coordinate Cs.

Monday, December 19th, 2016

I am completing my survey of the vote for molecule of the year candidates, which this year seems focused on chemical records of one type or another.

The first article[1] reports striving towards creating a molecule covering a complete column of the period table. In this case, group 7, containing N, P, As, Sb, Bi and Mc. Only the first four of these were incorporated, although the prospects of extending this to five seem good (and to six extremely unlikely).  The structure of this pnictogen chain is referenced here: DOI: 10.5517/CCDC.CSD.CC1LHPJ9 and I have demurred from a calculation.

The second article[2] relates to what might be called hypercoordination, and the achievement of what is felt is a maximum value of 16 to a single metal. I thought I might approach this one by searching the Cambridge structure database (CSD) by specifying any metal with a coordination number 16 as the search query. However, I was foiled in this query because the search software (Conquest) allows a maximum value of only 15! So instead I list the total number of hits retrieved for coordination numbers of 10-15: 25224, 4753, 8856, 2492, 839, 348 respectively.  

These totals have to be taken with some caution; the coordination number of what may often be very weak interactions may be often determined by human chemical perception rather than hard and fast rules. Nevertheless, the assignment of 348 molecules to having a coordination number of 15 is still a remarkably high number. If I can persuade CCDC to allow searches with 16, who knows what other candidates might emerge to rival this one, DOI: CCDC.CSD.CC1KFCQ2

The final candidate[3] is the only one where no measured coordinates are reported, with the title “Preparation of an ion with the highest calculated proton affinity: ortho-diethynylbenzene dianion”. There high level theoretical and computational modelling is reported to which I cannot add anything useful.

The common theme emerging of my review is that most of the candidates have crystal structures to which I have been able to occasionally add some computed quantum mechanical properties to try to tease out some other aspects of their character. It is also nice to be able to cite a persistent identifier (DOI) that leads directly to the 3D coordinates for the structures. My first ever post to this blog in 2008 addressed one solution on how such immediacy might be achieved and it is nice to see this now as a mainstream aspect of chemical publishing.

References

  1. A. Hinz, A. Schulz, and A. Villinger, "Synthesis of a Molecule with Four Different Adjacent Pnictogens", Chemistry – A European Journal, vol. 22, pp. 12266-12269, 2016. https://doi.org/10.1002/chem.201601916
  2. D. Pollak, R. Goddard, and K. Pörschke, "Cs[H<sub>2</sub>NB<sub>2</sub>(C<sub>6</sub>F<sub>5</sub>)<sub>6</sub>] Featuring an Unequivocal 16-Coordinate Cation", Journal of the American Chemical Society, vol. 138, pp. 9444-9451, 2016. https://doi.org/10.1021/jacs.6b02590
  3. B.L.J. Poad, N.D. Reed, C.S. Hansen, A.J. Trevitt, S.J. Blanksby, E.G. Mackay, M.S. Sherburn, B. Chan, and L. Radom, "Preparation of an ion with the highest calculated proton affinity: ortho-diethynylbenzene dianion", Chemical Science, vol. 7, pp. 6245-6250, 2016. https://doi.org/10.1039/c6sc01726f

Molecules of the year? The most polar neutral compound synthesized…

Sunday, December 18th, 2016

This, the fourth candidate provided by C&EN for a vote for the molecule of the year as discussed here, lays claim to the World’s most polar neutral molecule (system 1 shown below).[1] Here I explore a strategy for extending that record.

The claim for 1 (3 in [1]) is on the basis of its measured dipole moment which is 14.1± 0.7D in THF. This is qualified by the note that the dipole moment might be exalted by complex formation with dimethyl acetamide; the authors report a calculated smaller dipole moment of 9.6D (B3LYP/aug-cc-pVTZ) for the isolated molecule. 

Inspection of 1 suggests that it is impossible for both the amino groups to be co-planar with the benzene ring due to steric clashes between the H…H atoms and that they must be twisted to avoid this. If so, the conjugation with the ring would be reduced and so would the charge transfer from the amino groups to the cyano groups (the phenomenon responsible for the polarity). I re-optimised the molecule myself (ωB97XD/Def2-TZVPP/SCRF=THF) and it has C2 symmetry, with both amino groups rotated to avoid those steric H…H clashes (DOI: 10.14469/hpc/1989). The calculated dipole moment (the basis set is a bit better than in [1] and also the geometry is re-optimised in the solvent field) is 13.6D, which is rather closer to the measured value. An alternative explanation for the original mis-match between theory and experiment of 4.5D could be simply the lower quality basis set used in the calculation and no modelled geometric relaxation in the thf solvent field.

The NC bond lengths shown above will be used as a probe to reveal the extent of conjugation. I tried 2 (R=H), a method of avoiding the steric clash and allowing both amino groups to fully conjugate (DOI: 10.14469/hpc/1987). Note how the amino CN bond length contracts by 0.017Å, whereas the o-cyano CN lengths also contract slightly. The calculated dipole moment for this variation is 16.1D, which seems a rational outcome of increasing the conjugation. However, measured dipole mment values of 10.9 and 12.2D are reported for 2 (5a, R=Me and 5b C7H16) respectively.[1] This is surprising given that these systems avoid any NH…HN steric clash and should therefore allow better conjugation and hence an increased dipole moment. Perhaps it is these molecules rather than 1 where the measured dipole moment is perturbed by other effects?

Inspired by these molecules, I thought: why not start with a base aromatic ring that was already polar and sprinkle amino and cyano groups around it? Thus 3 and 4 above. The latter is derived from azulene, which is well-known to have a noticeable dipole moment of its own, with the five ring carrying excess charge to aspire to 6π-electron aromaticity and the seven ring losing charge to again create a 6π-aromatic ring. The cyano and amino groups would serve to stabilize those respective charges.

Firstly 4: Amino groups on the azulene 5,7 positions twist out of plane and do not conjugate (long NC bonds) but all the remaining groups show effective conjugation (DOI: 10.14469/hpc/1988). So one could probably dispense with 5,7-amino substitution. The calculated dipole moment is 21.4D, which elevates the previous value significantly.

Seven  2- or 3-substituted cyanoazulenes are known in the CSD (Cambridge structure database) and likewise seven 4, 6 or 8 nitrogen substituted derivatives are known. So it should be possible to combine these two groups onto an azulene ring.

Finally 3, where the amino CN bonds are even shorter, indicating increased stabilization of the cyclopropenium cation ring formed by charge transfer (DOI: 10.14469/hpc/1990). The amino groups no longer clash sterically. The central CC bond (nominally a double bond) is lengthened considerably to facilitate the charge transfer between rings and hence mutual aromatization, the five 5-ring bonds are 1.405Å (typical aromatic values) and the 3-ring 1.367-1.38Å (again aromatic values). This candidate has a dipole moment of 21.7D, despite its smaller size decreasing the separation of the charges and hence the moment.

If the function of a molecule of the year is to inspire ideas in others, this one has certainly achieved its purpose! Now for the syntheses!


Anionic systems always benefit from better basis sets, much more so than neutral or cationic molecules.

References

  1. J. Wudarczyk, G. Papamokos, V. Margaritis, D. Schollmeyer, F. Hinkel, M. Baumgarten, G. Floudas, and K. Müllen, "Hexasubstituted Benzenes with Ultrastrong Dipole Moments", Angewandte Chemie International Edition, vol. 55, pp. 3220-3223, 2016. https://doi.org/10.1002/anie.201508249